4YDD

Crystal structure of the perchlorate reductase PcrAB from Azospira suillum PS

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8101443	3000020	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	4Fe-4S ferredoxins	8101443	3000020	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	4Fe-4S ferredoxins	8101443	3000020	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Molydop_binding	e4yddC2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
C	NarG_1	e4yddC4	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: NarG_1	ECOD (1.6)
C	Molybdopterin_2nd	e4yddC3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
C	Molybdopterin_1st_1	e4yddC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
E	Molydop_binding	e4yddE2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
E	NarG_1	e4yddE4	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: NarG_1	ECOD (1.6)
E	Molybdopterin_2nd	e4yddE3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
E	Molybdopterin_1st_1	e4yddE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
A	Molydop_binding	e4yddA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: Molydop_binding	ECOD (1.6)
A	NarG_1	e4yddA4	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: NarG_1	ECOD (1.6)
A	Molybdopterin_2nd	e4yddA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
A	Molybdopterin_1st_1	e4yddA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)
B	Fer4_11	e4yddB2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
B	Nitr_red_bet_C_1	e4yddB1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Nitr_red_bet_C_1	ECOD (1.6)
D	Fer4_11	e4yddD1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
D	Nitr_red_bet_C_1	e4yddD2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Nitr_red_bet_C_1	ECOD (1.6)
F	Fer4_11	e4yddF2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_11	ECOD (1.6)
F	Nitr_red_bet_C_1	e4yddF1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Nitr_red_bet_C_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A, C, E	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
B, D, F	PF13247	4Fe-4S dicluster domain (Fer4_11)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	DMSO reductase family type II enzyme, molybdopterin subunit	oxidoreductase activity catalytic activity binding organic cyclic compound binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	protein-containing complex catalytic complex oxidoreductase complex cellular anatomical structure membrane
B, D, F	DMSO reductase family type II enzyme, iron-sulfur subunit	iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure membrane periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, C, E	IPR037943	Nitrate reductase alpha subunit-like, MopB domain	Domain
A, C, E	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A, C, E	IPR006656	Molybdopterin oxidoreductase	Domain
A, C, E	IPR017840	DMSO reductase family, type II, molybdopterin subunit	Family
A, C, E	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, C, E	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, C, E	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
B, D, F	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, D, F	IPR017839	DMSO reductase family, type II, iron-sulphur subunit	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.